arXiv subjects

Yiqiao Jin

Publications and source records attributed to Yiqiao Jin.

At least 37 records · Page 2Linked to original sources

arXiv2025

Topological Structure Learning Should Be A Research Priority for LLM-Based Multi-Agent Systems

Large Language Model-based Multi-Agent Systems (MASs) have emerged as a powerful paradigm for tackling complex tasks through collaborative intelligence. However, the topology of these systems--how agents in MASs should be configured, connected, and coordinated--remains largely unexplored. In this position paper, we call for a paradigm shift toward \emph{topology-aware MASs} that explicitly model and dynamically optimize the structure of inter-agent interactions. We identify three fundamental components--agents, communication links, and overall topology--that collectively determine the system's adaptability, efficiency, robustness, and fairness. To operationalize this vision, we introduce a systematic three-stage framework: 1) agent selection, 2) structure profiling, and 3) topology synthesis. This framework not only provides a principled foundation for designing MASs but also opens new research frontiers across language modeling, reinforcement learning, graph learning, and generative modeling to ultimately unleash their full potential in complex real-world applications. We conclude by outlining key challenges and opportunities in MASs evaluation. We hope our framework and perspectives offer critical new insights in the era of agentic AI.

cs.MA↗

arXiv2025

SARA: Selective and Adaptive Retrieval-augmented Generation with Context Compression

Retrieval-augmented Generation (RAG) extends large language models (LLMs) with external knowledge but faces key challenges: restricted effective context length and redundancy in retrieved documents. Pure compression-based approaches reduce input size but often discard fine-grained details essential for factual accuracy. We propose SARA, a unified RAG framework that balances local precision and global knowledge coverage under tight context budgets. SARA combines natural-language text snippets with semantic compression vectors to jointly enhance context efficiency and answer correctness. It represents contexts at two complementary levels: 1) fine-grained natural-language spans that preserve critical entities and numerical values, and 2) compact, interpretable vectors that summarize high-level semantics. An iterative evidence-selection module employs the compression vectors for dynamic reranking of contexts. Across 9 datasets and 5 open-source LLMs spanning 3 model families (Mistral, Llama, and Gemma), SARA consistently improves answer relevance (+17.71), answer correctness (+13.72), and semantic similarity (+15.53), demonstrating the importance of integrating textual and compressed representations for robust, context-efficient RAG.

cs.CL↗

arXiv2025

SciEvo: A 2 Million, 30-Year Cross-disciplinary Dataset for Temporal Scientometric Analysis

Understanding the creation, evolution, and dissemination of scientific knowledge is crucial for bridging diverse subject areas and addressing complex global challenges such as pandemics, climate change, and ethical AI. Scientometrics, the quantitative and qualitative study of scientific literature, provides valuable insights into these processes. We introduce SciEvo, a longitudinal scientometric dataset with over two million academic publications, providing comprehensive contents information and citation graphs to support cross-disciplinary analyses. SciEvo is easy to use and available across platforms, including GitHub, Kaggle, and HuggingFace. Using SciEvo, we conduct a temporal study spanning over 30 years to explore key questions in scientometrics: the evolution of academic terminology, citation patterns, and interdisciplinary knowledge exchange. Our findings reveal critical insights, such as disparities in epistemic cultures, knowledge production modes, and citation practices. For example, rapidly developing, application-driven fields like LLMs exhibit significantly shorter citation age (2.48 years) compared to traditional theoretical disciplines like oral history (9.71 years). Our data and analytic tools can be accessed at https://github.com/Ahren09/SciEvo.

cs.DL↗

arXiv2025

Reasoning Is Not All You Need: Examining LLMs for Multi-Turn Mental Health Conversations

Limited access to mental healthcare, extended wait times, and increasing capabilities of Large Language Models (LLMs) has led individuals to turn to LLMs for fulfilling their mental health needs. However, examining the multi-turn mental health conversation capabilities of LLMs remains under-explored. Existing evaluation frameworks typically focus on diagnostic accuracy and win-rates and often overlook alignment with patient-specific goals, values, and personalities required for meaningful conversations. To address this, we introduce MedAgent, a novel framework for synthetically generating realistic, multi-turn mental health sensemaking conversations and use it to create the Mental Health Sensemaking Dialogue (MHSD) dataset, comprising over 2,200 patient-LLM conversations. Additionally, we present MultiSenseEval, a holistic framework to evaluate the multi-turn conversation abilities of LLMs in healthcare settings using human-centric criteria. Our findings reveal that frontier reasoning models yield below-par performance for patient-centric communication and struggle at advanced diagnostic capabilities with average score of 31%. Additionally, we observed variation in model performance based on patient's persona and performance drop with increasing turns in the conversation. Our work provides a comprehensive synthetic data generation framework, a dataset and evaluation framework for assessing LLMs in multi-turn mental health conversations.

cs.CL↗

arXiv2025

The Influence of Text Variation on User Engagement in Cross-Platform Content Sharing

In today's cross-platform social media landscape, understanding factors that drive engagement for multimodal content, especially text paired with visuals, remains complex. This study investigates how rewriting Reddit post titles adapted from YouTube video titles affects user engagement. First, we build and analyze a large dataset of Reddit posts sharing YouTube videos, revealing that 21% of post titles are minimally modified. Statistical analysis demonstrates that title rewrites measurably improve engagement. Second, we design a controlled, multi-phase experiment to rigorously isolate the effects of textual variations by neutralizing confounding factors like video popularity, timing, and community norms. Comprehensive statistical tests reveal that effective title rewrites tend to feature emotional resonance, lexical richness, and alignment with community-specific norms. Lastly, pairwise ranking prediction experiments using a fine-tuned BERT classifier achieves 74% accuracy, significantly outperforming near-random baselines, including GPT-4o. These results validate that our controlled dataset effectively minimizes confounding effects, allowing advanced models to both learn and demonstrate the impact of textual features on engagement. By bridging quantitative rigor with qualitative insights, this study uncovers engagement dynamics and offers a robust framework for future cross-platform, multimodal content strategies.

cs.SI↗

arXiv2025

ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding

Understanding biological processes, drug development, and biotechnological advancements requires a detailed analysis of protein structures and functions, a task that is inherently complex and time-consuming in traditional protein research. To streamline this process, we introduce ProteinGPT, a state-of-the-art multimodal large language model for proteins that enables users to upload protein sequences and/or structures for comprehensive analysis and responsive inquiries. ProteinGPT integrates protein sequence and structure encoders with linear projection layers to ensure precise representation adaptation and leverages a large language model (LLM) to generate accurate, contextually relevant responses. To train ProteinGPT, we constructed a large-scale dataset of 132,092 proteins, each annotated with 20-30 property tags and 5-10 QA pairs per protein, and optimized the instruction-tuning process using GPT-4o. Experiments demonstrate that ProteinGPT effectively generates informative responses to protein-related questions, achieving high performance on both semantic and lexical metrics and significantly outperforming baseline models and general-purpose LLMs in understanding and responding to protein-related queries. Our code and data are available at https://github.com/ProteinGPT/ProteinGPT.

cs.AI↗

arXiv2025

Large Language Model Agent: A Survey on Methodology, Applications and Challenges

The era of intelligent agents is upon us, driven by revolutionary advancements in large language models. Large Language Model (LLM) agents, with goal-driven behaviors and dynamic adaptation capabilities, potentially represent a critical pathway toward artificial general intelligence. This survey systematically deconstructs LLM agent systems through a methodology-centered taxonomy, linking architectural foundations, collaboration mechanisms, and evolutionary pathways. We unify fragmented research threads by revealing fundamental connections between agent design principles and their emergent behaviors in complex environments. Our work provides a unified architectural perspective, examining how agents are constructed, how they collaborate, and how they evolve over time, while also addressing evaluation methodologies, tool applications, practical challenges, and diverse application domains. By surveying the latest developments in this rapidly evolving field, we offer researchers a structured taxonomy for understanding LLM agents and identify promising directions for future research. The collection is available at https://github.com/luo-junyu/Awesome-Agent-Papers.

cs.CL↗

arXiv2025

ScreenLLM: Stateful Screen Schema for Efficient Action Understanding and Prediction

Graphical User Interface (GUI) agents are autonomous systems that interpret and generate actions, enabling intelligent user assistance and automation. Effective training of these agent presents unique challenges, such as sparsity in supervision signals, scalability for large datasets, and the need for nuanced user understanding. We propose stateful screen schema, an efficient representation of GUI interactions that captures key user actions and intentions over time. Building on this foundation, we introduce ScreenLLM, a set of multimodal large language models (MLLMs) tailored for advanced UI understanding and action prediction. Extensive experiments on both open-source and proprietary models show that ScreenLLM accurately models user behavior and predicts actions. Our work lays the foundation for scalable, robust, and intelligent GUI agents that enhance user interaction in diverse software environments.

cs.CL↗

arXiv2025

Protein Large Language Models: A Comprehensive Survey

Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or applications, this work provides the first comprehensive overview of Protein LLMs, covering their architectures, training datasets, evaluation metrics, and diverse applications. Through a systematic analysis of over 100 articles, we propose a structured taxonomy of state-of-the-art Protein LLMs, analyze how they leverage large-scale protein sequence data for improved accuracy, and explore their potential in advancing protein engineering and biomedical research. Additionally, we discuss key challenges and future directions, positioning Protein LLMs as essential tools for scientific discovery in protein science. Resources are maintained at https://github.com/Yijia-Xiao/Protein-LLM-Survey.

q-bio.BM↗

arXiv2025

UniGuard: Towards Universal Safety Guardrails for Jailbreak Attacks on Multimodal Large Language Models

Multimodal large language models (MLLMs) have revolutionized vision-language understanding but remain vulnerable to multimodal jailbreak attacks, where adversarial inputs are meticulously crafted to elicit harmful or inappropriate responses. We propose UniGuard, a novel multimodal safety guardrail that jointly considers the unimodal and cross-modal harmful signals. UniGuard trains a multimodal guardrail to minimize the likelihood of generating harmful responses in a toxic corpus. The guardrail can be seamlessly applied to any input prompt during inference with minimal computational costs. Extensive experiments demonstrate the generalizability of UniGuard across multiple modalities, attack strategies, and multiple state-of-the-art MLLMs, including LLaVA, Gemini Pro, GPT-4o, MiniGPT-4, and InstructBLIP. Notably, this robust defense mechanism maintains the models' overall vision-language understanding capabilities.

cs.CL↗

arXiv2025

CultureVLM: Characterizing and Improving Cultural Understanding of Vision-Language Models for over 100 Countries

Vision-language models (VLMs) have advanced human-AI interaction but struggle with cultural understanding, often misinterpreting symbols, gestures, and artifacts due to biases in predominantly Western-centric training data. In this paper, we construct CultureVerse, a large-scale multimodal benchmark covering 19, 682 cultural concepts, 188 countries/regions, 15 cultural concepts, and 3 question types, with the aim of characterizing and improving VLMs' multicultural understanding capabilities. Then, we propose CultureVLM, a series of VLMs fine-tuned on our dataset to achieve significant performance improvement in cultural understanding. Our evaluation of 16 models reveals significant disparities, with a stronger performance in Western concepts and weaker results in African and Asian contexts. Fine-tuning on our CultureVerse enhances cultural perception, demonstrating cross-cultural, cross-continent, and cross-dataset generalization without sacrificing performance on models' general VLM benchmarks. We further present insights on cultural generalization and forgetting. We hope that this work could lay the foundation for more equitable and culturally aware multimodal AI systems.

cs.AI↗

arXiv2024

RNA-GPT: Multimodal Generative System for RNA Sequence Understanding

RNAs are essential molecules that carry genetic information vital for life, with profound implications for drug development and biotechnology. Despite this importance, RNA research is often hindered by the vast literature available on the topic. To streamline this process, we introduce RNA-GPT, a multi-modal RNA chat model designed to simplify RNA discovery by leveraging extensive RNA literature. RNA-GPT integrates RNA sequence encoders with linear projection layers and state-of-the-art large language models (LLMs) for precise representation alignment, enabling it to process user-uploaded RNA sequences and deliver concise, accurate responses. Built on a scalable training pipeline, RNA-GPT utilizes RNA-QA, an automated system that gathers RNA annotations from RNACentral using a divide-and-conquer approach with GPT-4o and latent Dirichlet allocation (LDA) to efficiently handle large datasets and generate instruction-tuning samples. Our experiments indicate that RNA-GPT effectively addresses complex RNA queries, thereby facilitating RNA research. Additionally, we present RNA-QA, a dataset of 407,616 RNA samples for modality alignment and instruction tuning, further advancing the potential of RNA research tools.

q-bio.GN↗

arXiv2024

PrivacyMind: Large Language Models Can Be Contextual Privacy Protection Learners

The proliferation of Large Language Models (LLMs) has driven considerable interest in fine-tuning them with domain-specific data to create specialized language models. Nevertheless, such domain-specific fine-tuning data often contains contextually sensitive personally identifiable information (PII). Direct fine-tuning of LLMs on this data without privacy protection poses a risk of data leakage of sensitive PII during inference time. To address this challenge, we introduce Contextual Privacy Protection Language Models (PrivacyMind), a novel paradigm for fine-tuning LLMs that effectively injects domain-specific knowledge while safeguarding inference-time data privacy. Our work offers a theoretical analysis for model design and benchmarks various techniques such as corpus curation, penalty-based unlikelihood in training loss, instruction-based tuning, etc. Extensive experiments across diverse datasets and scenarios demonstrate the effectiveness of our approaches. In particular, instruction tuning with both positive and negative examples stands out as a promising method, effectively protecting private data while enhancing the model's knowledge. Our work underscores the potential for Large Language Models as robust contextual privacy protection learners. The complete code and data for the work can be found at https://github.com/Yijia-Xiao/PrivacyMind.

cs.CL↗

arXiv2024

Deconstructing The Ethics of Large Language Models from Long-standing Issues to New-emerging Dilemmas: A Survey

Large Language Models (LLMs) have achieved unparalleled success across diverse language modeling tasks in recent years. However, this progress has also intensified ethical concerns, impacting the deployment of LLMs in everyday contexts. This paper provides a comprehensive survey of ethical challenges associated with LLMs, from longstanding issues such as copyright infringement, systematic bias, and data privacy, to emerging problems like truthfulness and social norms. We critically analyze existing research aimed at understanding, examining, and mitigating these ethical risks. Our survey underscores integrating ethical standards and societal values into the development of LLMs, thereby guiding the development of responsible and ethically aligned language models.

cs.CL↗

arXiv2024

MM-Soc: Benchmarking Multimodal Large Language Models in Social Media Platforms

Social media platforms are hubs for multimodal information exchange, encompassing text, images, and videos, making it challenging for machines to comprehend the information or emotions associated with interactions in online spaces. Multimodal Large Language Models (MLLMs) have emerged as a promising solution to these challenges, yet they struggle to accurately interpret human emotions and complex content such as misinformation. This paper introduces MM-Soc, a comprehensive benchmark designed to evaluate MLLMs' understanding of multimodal social media content. MM-Soc compiles prominent multimodal datasets and incorporates a novel large-scale YouTube tagging dataset, targeting a range of tasks from misinformation detection, hate speech detection, and social context generation. Through our exhaustive evaluation on ten size-variants of four open-source MLLMs, we have identified significant performance disparities, highlighting the need for advancements in models' social understanding capabilities. Our analysis reveals that, in a zero-shot setting, various types of MLLMs generally exhibit difficulties in handling social media tasks. However, MLLMs demonstrate performance improvements post fine-tuning, suggesting potential pathways for improvement. Our code and data are available at https://github.com/claws-lab/MMSoc.git.

cs.CL↗

arXiv2024

Towards Fair Graph Anomaly Detection: Problem, Benchmark Datasets, and Evaluation

The Fair Graph Anomaly Detection (FairGAD) problem aims to accurately detect anomalous nodes in an input graph while avoiding biased predictions against individuals from sensitive subgroups. However, the current literature does not comprehensively discuss this problem, nor does it provide realistic datasets that encompass actual graph structures, anomaly labels, and sensitive attributes. To bridge this gap, we introduce a formal definition of the FairGAD problem and present two novel datasets constructed from the social media platforms Reddit and Twitter. These datasets comprise 1.2 million and 400,000 edges associated with 9,000 and 47,000 nodes, respectively, and leverage political leanings as sensitive attributes and misinformation spreaders as anomaly labels. We demonstrate that our FairGAD datasets significantly differ from the synthetic datasets used by the research community. Using our datasets, we investigate the performance-fairness trade-off in nine existing GAD and non-graph AD methods on five state-of-the-art fairness methods. Our code and datasets are available at https://github.com/nigelnnk/FairGAD

cs.SI↗

arXiv2024

Prototypical Reward Network for Data-Efficient RLHF

The reward model for Reinforcement Learning from Human Feedback (RLHF) has proven effective in fine-tuning Large Language Models (LLMs). Notably, collecting human feedback for RLHF can be resource-intensive and lead to scalability issues for LLMs and complex tasks. Our proposed framework Proto-RM leverages prototypical networks to enhance reward models under limited human feedback. By enabling stable and reliable structural learning from fewer samples, Proto-RM significantly enhances LLMs' adaptability and accuracy in interpreting human preferences. Extensive experiments on various datasets demonstrate that Proto-RM significantly improves the performance of reward models and LLMs in human feedback tasks, achieving comparable and usually better results than traditional methods, while requiring significantly less data. in data-limited scenarios. This research offers a promising direction for enhancing the efficiency of reward models and optimizing the fine-tuning of language models under restricted feedback conditions.

cs.CL↗

arXiv2024

Empowering Interdisciplinary Insights with Dynamic Graph Embedding Trajectories

We developed DyGETViz, a novel framework for effectively visualizing dynamic graphs (DGs) that are ubiquitous across diverse real-world systems. This framework leverages recent advancements in discrete-time dynamic graph (DTDG) models to adeptly handle the temporal dynamics inherent in dynamic graphs. DyGETViz effectively captures both micro- and macro-level structural shifts within these graphs, offering a robust method for representing complex and massive dynamic graphs. The application of DyGETViz extends to a diverse array of domains, including ethology, epidemiology, finance, genetics, linguistics, communication studies, social studies, and international relations. Through its implementation, DyGETViz has revealed or confirmed various critical insights. These include the diversity of content sharing patterns and the degree of specialization within online communities, the chronological evolution of lexicons across decades, and the distinct trajectories exhibited by aging-related and non-related genes. Importantly, DyGETViz enhances the accessibility of scientific findings to non-domain experts by simplifying the complexities of dynamic graphs. Our framework is released as an open-source Python package for use across diverse disciplines. Our work not only addresses the ongoing challenges in visualizing and analyzing DTDG models but also establishes a foundational framework for future investigations into dynamic graph representation and analysis across various disciplines.

cs.LG↗